Question: download/cache ensembl biomaRt data for genes and their annotations?
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gravatar for biocyberman
2.7 years ago by
biocyberman760
Denmark
biocyberman760 wrote:

I am working with human and rat gene sets. From a list of ensembl gene IDs, I want to retrieve columns of attributes via biomaRt. With about 4000 genes, the process runs very slowly (30 minutes). I can save the R object and use it for next times. But is there anyway for me to download a whole package of gene annotation information with gen ontology, RFAM, PFAM, Interpro, etc? In particular, I am interested in downloading the following attitutes.

This is a snippet for what I am trying to do:

library(biomaRt)
#Example of 20 gene ids.
 ensids <- c(
'ENSRNOG00000000001', 
'ENSRNOG00000000009', 
'ENSRNOG00000000040', 
'ENSRNOG00000000055', 
'ENSRNOG00000000082', 
'ENSRNOG00000000091', 
'ENSRNOG00000000129', 
'ENSRNOG00000000137', 
'ENSRNOG00000000138', 
'ENSRNOG00000000142', 
'ENSRNOG00000000156', 
'ENSRNOG00000000187', 
'ENSRNOG00000000196', 
'ENSRNOG00000000231', 
'ENSRNOG00000000233', 
'ENSRNOG00000000239', 
'ENSRNOG00000000277', 
'ENSRNOG00000000288', 
'ENSRNOG00000000307', 
'ENSRNOG00000000321')

m <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "rnorvegicus_gene_ensembl")

enstable <- getBM(mart = m, attributes = c('ensembl_gene_id','gene_biotype',
                                       'external_gene_name', 'superfamily',
                                       'family', 'go_id','goslim_goa_accession',
                                       'rfam', 'pirsf','interpro','tigrfam'),
              filters = c('ensembl_gene_id'), values = ensids)

Even though the first time download may take more time, but I see much greater benefits of subsequent uses: leave the ensembl server unstressed with repeated queries, shorter runtime, and internet independent.

biomart ensembl • 689 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by biocyberman760
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